EMEN Documentation
Welcome to Electron Microscopy Electronic Notebook. Your project is assigned to a specific project title. Only authorized co-investigators have access to the information on this project Notebook. Not everyone has the privilege to delete or modify the information recorded in the Notebook. As the project expands, there will be other subprojects, which may include different personnel who may be allowed to have access only to different subprojects.
The sole purpose of the Notebook is to help keeping track the experimental conditions from biochemical purification, to specimen freezing and imaging conditions. This informatics will allow multiple co-investigators in remote sites to share a common notebook and facilitate the problem tracking in case that the projects encounter difficulties. The followings information are included in the Notebook and you must fill in accordingly:
1.Specimen Purification: it is critical that the specimen supplier will enter the requested information on how the specimen was purified, how concentrated the specimen was made, what buffer it was kept and what conditions it should be stored. These will help the microscopists to understand the chemical nature of the specimen. It is our experience that the buffer conditions can influence the success in making good or bad grid for cryoEM. The suitability of the specimen for cryoEM definitely depends on the structural uniformtiy of the specimen, which may be dependent on the biochemical purification steps or buffer/ligand conditions. Therefore, the specimen supplier must enter these informations for each time when a specimen is sent to NCMI.
2.Specimen freezing: We have different ways of freezing the specimen including a computer-controlled apparatus called Vitribot. Different parameters may be used to freeze the specimen, which will influence the outcome of the grid quality. It is our intention to search systematically the optimal freezing parameters and maximum reproducibility for your specimen. Therefore, all microscopists must fill in the freezing conditions and the type and treatment of grids used for each experiment.
3.Microscopy session: We intend to record all the imaging conditions used for acquiring the cryoEM data. This information is necessary when we prepare the manuscript upon completing the project and also allows future co-investigators to repeat or follow up other experiments of the same specimen. In addition, this can allow us to mine the data in the future as how to get the best data and to explain why some data are better than the others. This is a large scale and long-term effort that NCMI is undertaking to improve the efficiency of data collection.
4.Labnote: This is a very handy option that allows each co-investigators to jolt down information as one would normally do so in a paper notebook. This will allow co-investigator to paste experimental data for other co-investigators to see. This can be a protein gel, an electron micrograph or a preliminary structure.
5.References: It will be very useful if the co-investigators will list relevant literatures or provide pdf of relevant papers.
6.Publications: We want to archive all the published papers and also the figures and text of papers to be submitted for publication.
7.Structural factor: This will be the experimentally or theoretically derived one-dimensional scattering curve for the specimen under investigation.
